MolNFT v1 · #60837 · protein
Crystal structure of tRNA DELTA(2)-isopentenylpyrophosphate transferase (SE0981) from staphylococcus epidermidis. northeast structural genomics consortium target SER100
3D3Q: “Crystal structure of tRNA DELTA(2)-isopentenylpyrophosphate transferase (SE0981) from staphylococcus…”. X-ray diffraction, 8 pockets (best druggability 0.80). MolNFT v1 #60837 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3D3Q
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA DELTA(2)-isopentenylpyrophosphate transferase
- EC
- 2.5.1.8
- UniProt
- Q8CQL3
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 307 | 54% helix, 11% strand | Q8CQL3 |
| B | TRNA DELTA(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) | protein | 303 | 52% helix, 11% strand | Q8CQL3 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.80 | 0.91 | 56 | empty |
| 2 | 414 | 0.80 | 0.88 | 62 | empty |
| 3 | 528 | 0.73 | 0.81 | 53 | empty |
| 4 | 546 | 0.64 | 0.76 | 51 | empty |
| 5 | 114 | 0.60 | 0.86 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 3D3Q · Crystal structure of tRNA delta(2)-isopentenylpyrophosphate transferase (SE0981) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CQL3 · AlphaFold monomer V2.0 prediction for tRNA dimethylallyltransferase (Q8CQL3) · a predicted model of the same protein · chain B against A, TM-score 0.77
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8CQL3
- Elsewhere: RCSB PDB 3D3Q · PDBe 3D3Q · UniProt Q8CQL3
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